Metadata-Version: 2.4
Name: micro_sam
Version: 1.8.1
Summary: Segment Anything For Microscopy
Home-page: https://github.com/computational-cell-analytics/micro-sam
Author: Anwai Archit, Paul Hilt, Genevieve Buckley, Constantin Pape
License: MIT
Project-URL: Bug Tracker, https://github.com/computational-cell-analytics/micro-sam/issues
Project-URL: Documentation, https://computational-cell-analytics.github.io/micro-sam/micro_sam.html
Project-URL: Source Code, https://github.com/computational-cell-analytics/micro-sam
Project-URL: User Support, https://github.com/computational-cell-analytics/micro-sam/issues
Classifier: Development Status :: 5 - Production/Stable
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bioimage-cpp>=0.3
Requires-Dist: bioimageio.core
Requires-Dist: h5py
Requires-Dist: imagecodecs
Requires-Dist: imageio
Requires-Dist: joblib
Requires-Dist: kornia
Requires-Dist: magicgui
Requires-Dist: matplotlib
Requires-Dist: napari<0.7
Requires-Dist: natsort
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pooch
Requires-Dist: PyQt5
Requires-Dist: python-elf>=0.9
Requires-Dist: scikit-image
Requires-Dist: scikit-learn
Requires-Dist: segment-anything
Requires-Dist: superqt
Requires-Dist: timm
Requires-Dist: torch>=2.5
Requires-Dist: torch-em>=0.9
Requires-Dist: torchvision
Requires-Dist: tqdm
Requires-Dist: trackastra>=0.5.3
Requires-Dist: xarray
Requires-Dist: xxhash
Requires-Dist: zarr
Dynamic: license-file

[![DOC](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://computational-cell-analytics.github.io/micro-sam/)
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# Segment Anything for Microscopy

<a href="https://github.com/computational-cell-analytics/micro-sam"><img src="https://github.com/computational-cell-analytics/micro-sam/blob/main/doc/logo/logo_and_text.png" width="300" align="right">

Tools for segmentation and tracking in microscopy build on top of [Segment Anything](https://segment-anything.com/).
Segment and track objects in microscopy images interactively with a few clicks!

We implement napari applications for:
- interactive 2d segmentation (Left: interactive cell segmentation)
- interactive 3d segmentation (Middle: interactive mitochondria segmentation in EM)
- interactive tracking of 2d image data (Right: interactive cell tracking)

<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/d04cb158-9f5b-4460-98cd-023c4f19cccd" width="256">
<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/dfca3d9b-dba5-440b-b0f9-72a0683ac410" width="256">
<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/aefbf99f-e73a-4125-bb49-2e6592367a64" width="256">

If you run into any problems or have questions regarding our tool please open an [issue](https://github.com/computational-cell-analytics/micro-sam/issues/new/choose) on Github or reach out via [image.sc](https://forum.image.sc/) using the tag `micro-sam`, and tagging [@constantinpape](https://forum.image.sc/u/constantinpape/summary) and [@anwai98](https://forum.image.sc/u/anwai98/summary).
You can follow recent updates on `micro_sam` in our [news feed](https://forum.image.sc/t/microsam-news-feed).

## Installation and Usage

Please check [the documentation](https://computational-cell-analytics.github.io/micro-sam/) for details on how to install and use `micro_sam`. You can also watch [the quickstart video](https://youtu.be/gcv0fa84mCc), [our virtual I2K workshop video](https://www.youtube.com/watch?v=dxjU4W7bCis&list=PLdA9Vgd1gxTbvxmtk9CASftUOl_XItjDN&index=33) or [all video tutorials](https://youtube.com/playlist?list=PLwYZXQJ3f36GQPpKCrSbHjGiH39X4XjSO&si=qNbB8IFXqAX33r_Z).


## Contributing

We welcome new contributions!

If you are interested in contributing to `micro-sam`, please see the [contributing guide](https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#contribution-guide). The first step is to [discuss your idea in a new issue](https://github.com/computational-cell-analytics/micro-sam/issues/new) with the current developers.


## Citation

If you are using this repository in your research please cite
- our [paper](https://www.nature.com/articles/s41592-024-02580-4) (now published in Nature Methods!)
- and the original [Segment Anything publication](https://arxiv.org/abs/2304.02643).
- If you use `vit-tiny` models please also cite [Mobile SAM](https://arxiv.org/abs/2306.14289).
- If you use automatic tracking, please also cite [Trackastra](https://arxiv.org/abs/2405.15700).


## Related Projects

There are a few other napari plugins build around Segment Anything:
- https://github.com/MIC-DKFZ/napari-sam (2d and 3d support)
- https://github.com/royerlab/napari-segment-anything (only 2d support)
- https://github.com/hiroalchem/napari-SAM4IS

Compared to these we support more applications (2d, 3d and tracking), and provide finetuning methods and finetuned models for microscopy data.
[WebKnossos](https://webknossos.org/) and [QuPath](https://qupath.github.io/) also offer integration of Segment Anything for interactive segmentation.

We have also built follow-up work that is based on `micro_sam`:
- https://github.com/computational-cell-analytics/patho-sam - improves SAM for histopathology.
- https://github.com/computational-cell-analytics/medico-sam - improves SAM for medical imaging.
- https://github.com/computational-cell-analytics/peft-sam - studies parameter efficient fine-tuning for SAM.

## Release Overview

You can find an overview of changes introduced in previous releases [here](https://github.com/computational-cell-analytics/micro-sam/blob/main/RELEASE_OVERVIEW.md).
